Pr Present enters ers: : Yu Xiaoyu, Zhang Shu, Wang Xuan, Hou - PowerPoint PPT Presentation

Pr Present enters ers: : Yu Xiaoyu, Zhang Shu, Wang Xuan, Hou Yuelong

Background Utilization World Chemical Ratio: Population: Fertilizer: 30- 40% 7 billion $185 billion absorbed Fertilize Directional Directionally Fertilization Peanuts with Molybdenate

Introduction – New version of Prometheus • Sensor Protein • Simulation

Project Outline Human Collecting Delivery Kill Switch Simulation Practice Mo • Mechanism • Mechanism • Mechanism • Design • Design • Parameters • Mechanism • Results • Next Step • Results and • Design Analysis • Results • Discussion Directional Simulation Bacterial Fertilizer

Project Outline Human Collecting Delivery Kill Switch Simulation Practice Mo • Mechanism • Mechanism • Mechanism • Design • Design • Parameters • Mechanism • Results • Next Step • Results and • Design Analysis • Results • Discussion

E.coli Prometheus collect Mo • Absorb Mo by INPN-ModA Aim • ModA/INP Mechanism • ModA Design parts • INPN+eYFP/INPN+ModA • Expression and Results purification of ModA

ModA: periplasmic ModA ： INP: Surfave display  Highest substrate system Kd values  Periplasmic Hollenstein K, Frei D C, Locher K P. Nature, 2007, 446(7132): 213-216 .

Clone, expression and purification of ModA Part: eliminate some sites of endonucleases Left : expression and Right : ModA purification of ModA binding Mo

Design part: INPN+eYFP & INPN+ModA INPN > INPNC: the activity of small passenger Future plan: fusion protein

Project Outline Human Collecting Delivery Kill Switch Simulation Practice Mo • Mechanism • Mechanism • Mechanism • Design • Design • Parameters • Mechanism • Results • Next Step • Results and • Design Analysis • Results • Discussion

Delivery system • Deliver Mo to roots Aim • Chemoreceptor Mechanism • Chemotaxis • McfR Design parts • Chemotaxis towards Results malate & succinate

Mechanism: Chemoreceptor & chemotaxis Malate succinate McfR

Design part: McfR Chassis: BL21 Insulator McfR Promoter RBS BBa_J23100

Result: Chemotaxis towards malate/succinate Coating contents of capillary tubes

Result: Chemotaxis towards malate/succinate PR5a ： promoter&RBS PA2652 ： 2011-Imperial London No chemotaxis More universal function

Identical manner & conserved sequence Attractants ： McpS － LBR ＋ Chemorecptors: P. putida malate / succinate KT2440 pp4658 Conserved Conserved sequences assemble a super E.coli Prometheus Pineda-Molina, Estela, et al. Proceedings of the National Academy of Sciences 109.46 (2012): 18926-18931.

Project Outline Human Collecting Delivery Kill Switch Simulation Practice Mo • Mechanism • Mechanism • Mechanism • Design • Design • Parameters • Mechanism • Results • Next Step • Results and • Design Analysis • Results • Discussion

Kill Switch – Time Bomb • Trigger suicide spontaneously Aim at a certain time • MazF toxin protein Mechanism • Genetic circuit Design • Deal with background inference Next Step • Model “Countdown Time”

Kill Switch – Time Bomb: Circuit IPTG 1 LacI 0 Stable State CI 1 MazF 0

Kill Switch – Time Bomb: Circuit IPTG 0 LacI 1 CI 0 Suicide State MazF 1

Kill Switch – Time Bomb: Next Step Background Inference: Model “Countdown Time” • Knock out l acI and MazEF system • LacI accumulation speed • Test CI • Repression Threshold of Promoter 2

Project Outline Human Collecting Delivery Kill Switch Simulation Practice Mo • Mechanism • Mechanism • Mechanism • Design • Design • Parameters • Mechanism • Results • Next Step • Results and • Design Analysis • Results • Discussion

Simulation • Simulate of E.coil Aim chemotaxis in soil • 3 steps Built • Parameters • Get E.coil chemotaxis Result curve • Review Next Step • Forecast

Sketch map: E.coil chemotaxis in soil

Nothing at first

1 st step: Virtual Peanut Root

1 st step: Virtual Peanut Root

2 nd step: Exudates’ spatial distribution

2 nd step: Exudates’ spatial distribution Sauer, D., Kuzyakov, Y. & Stahr, K. J. Plant Nutr. Soil Sci 169 , 360-362 (2006).

3 rd step: E.coil Motion

3 rd step: E.coil Motion

Parameters Parameter Value Origin 10μm/s Velocity Berg, H.C.(ED.).(2004). E.coil in Motion. Springer run 1.4s run 3.0s Brown, D.A.,& Berg, H.C., tumble 0.14s PANS , 1974, 71(4), 1388-1392 tumble 0.19s Exudate distribution Shown above Estimation formula K D 3.5mM Fit from wet experiment Surface -15, -4, -3, -2, - Set order concentration(lg) 1 M

Parameters: Get K D Brown, D. A. & Berg, H. C. PNAS, 71 , 1388-1392 (1974).

A complete model

A complete model: Visualization The screenshots of the visualized program Violet points tend towards root

Simulation 1000 bacteria 1 hour 5*5*5 cm 3 root space

Result: Get E.coil chemotaxis curve 1 hour

Calculate economic effectiveness 80% 40%

Find E.coli 's best suicide time ~2500 sec

Compare dry & wet lab results Bell-shaped curves

Difference of our model and real world

Forecast Simple, but innovative! Put the influence of the complex environment into our model

Forecast A little step of simulation, a new view of synthetic biology.

Project Outline Human Collecting Delivery Kill Switch Simulation Practice Mo • Mechanism • Mechanism • Mechanism • Design • Design • Parameters • Mechanism • Results • Next Step • Results and • Design Analysis • Results • Discussion

Policy & Practice Edu-justice Bio-policy Three Three Public Promotion “E”s “C”s

Policy & Practice Highlights ! Human practice Edu-justice Change Bio-Policy Policy & Practice

Policy & Practice ? Social Why BNU? Edu-justice Education Beijing Normal More than 100 years University!

Policy & Practice : Edu-justice Rural Areas in Shandong Urban Areas in Beijing 2014, August 2014, November Lectures: Biology, synthetic biology and iGEM Participate Members: Wang Xuan, Huang Li, Liu Bing, Huang Shengnan, Li Siyao, Ma Di

Policy & Practice : Edu-justice Answer by 47 senior high students in rural areas and 27 in urban areas 17 % still received no lab courses About 70% do not know any subareas

Policy & Practice : Edu-justice Education inequality !

Policy & Practice : Edu-justice

Policy & Practice : Bio-policy Wang Yue BNU-China team members The director of the journal of with Wang Yue Chinese Health Law 1. Literature 2.Interviewed 3.Suggestions Wang Yue giving Review

Policy & Practice Three “E”s Three “C”s Pub Promotion

Policy & Practice : Three “E”s Environment Economy Efficiency Module Literature Review Interview

Policy & Practice : Three “C”s Conference Communication Collaboration Shandong Academy China iGEM Meet Kyoto, Peking, of Agricultural up in Wuhan OUC team Science

Policy & Practice : Public Promotion Open Day of Future iGEMers Rural Project BNU-China August Oct Oct Weifang Shidaerfu BNU

Acknowledgements Prof. Zhu Xudong, Prof. Yang Dong and Xiang benqiong Support us to our iGEM journey. Huo liang, Ren qidong & Zhang yahui Gave us advises doing experiment. Dr.Du Guoguang and an Zhao Shifeng, Helped us doing laser scanning of peanuts’ roots. Dai Cong and his family, Helped us get peanuts samples. Prof. Wang Yingdian Gave us advise about our bright future.